tbuckley/cabot-search huggingface dataset:
EPCO-32. DISSECTING THE INTRA- AND INTER-TUMORAL HETEROGENEITY UNDERLYING GLIOBLASTOMA PATHOGENESIS UTILIZING MULTI-OMICS ANALYSIS
Authors: Takuma Nakashima, Yusuke Funakoshi, Hirohisa Yajima, Ryo Yamamoto, Yuriko Sugihara, Shohei Nambu, Yoshiki Arakawa, Shota Tanaka, Joji Ishida, Ryuta Saito, Ryosuke Hanaya, Koji Yoshimoto, Yoshitaka Narita, Hiromichi Suzuki
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM) is the most common malignant brain tumor with a dismal prognosis. Considering its extensive molecular diversity underlies therapeutic resistance to multimodal treatment, it is imperative to reveal intra- and inter-tumoral heterogeneity, leading to further understanding of GBM pathogenesis. We analyzed 289 whole-genome sequencing data (WGS) including 159 unpublished deep WGS (≥ ×120 coverage) along with RNA-seq, DNA methylation array, whole-genome bisulfite sequencing, and assay for transposase-accessible chromatin with sequencing (ATAC-seq) to uncover the multi-omics molecular heterogeneity of GBM. Along with inter-tumoral heterogeneity of genetic driver alterations, deep WGS enables us to delineate a fine view of clonal architecture where mutational signatures differ across clonal and subclonal mutations, supporting that different mutational processes contribute to GBM pathogenesis depending on the developmental stage. As well, tumor cell differentiation status detected by transcriptional deconvolution analysis is associated with multi-layer profiles including genome, transcriptome, epigenome, and chromatin status. ATAC-seq demonstrated distinct features of genome-wide chromatin accessibility associated with gene expression subtypes of GBM. Motif enrichment analysis detects the differentially accessible regions where the proneural subtypes are enriched with the SOX10 motif, known as a transcription factor for mesenchymal transition whereas the mesenchymal and classical subtypes are enriched with the CREB/ATF motif, a regulator of TGF beta associated with a poor prognosis. Our findings support a model in which GBM evolves through generating genetic and epigenetic intra-tumoral heterogeneity suggesting that specific cell states may have distinct vulnerability to mutational processes and epigenetic modifications. Our analysis reveals the molecular mechanisms underlying the progression of GBM enhancing our understanding of the pathogenesis.
EPID-26. THE IMPACT OF COVID-19 POSITIVITY AND PREVALENCE ON TREATMENT UTILIZATION FOR GLIOBLASTOMA PATIENTS
Authors: Ping Zhu, Clark Chen
Journal: Neuro-Oncology (2023)

Abstract OBJECTIVES Glioblastoma (GBM) is the most common (46.1%) and aggressive malignant primary brain tumor. We propose to explore the pandemic effect on the change of health care delivery for glioblastoma patients using the National Cancer Database (NCDB) and validate the findings in primary brain tumors using one of the largest COVID-19 real-time centralized data in the world - the National COVID Cohort Collaborative (N3C) database. METHODS Multivariable binary logistic regression models were performed to investigate whether the pandemic (including COVID-19 positivity and density of COVID-19 prevalence based on zip code-level) affected the receipt of GBM care including surgical procedure, radiation, and chemotherapy. RESULTS A total of 4093 GBM patients and 4481 primary brain tumor patients were derived from the NCDB and N3C, respectively. Seventy-nine percent of GBM patients received the COVID-19 test (3241/4093) and 290 patients were COVID-19 positive. Black, Hispanic, lower education-level, and higher Charlson/Deyo Score ( &amp;gt;=2) were significant factors related to COVID-19 positivity. The proportions of receiving GBM care significantly decreased in COVID-19-positive patients compared to pre-pandemic years (2018-2019). After adjusting the potential confounders and covariates, the odds of undergoing tumor resection/biopsy (aOR-0.37, p&amp;lt; 0.001), radiation (aOR-0.36, p&amp;lt; 0.001), and chemotherapy (aOR-0.31, p&amp;lt; 0.001) for COVID-19 positive patients were significantly lower than COVID-19 negative patients (NCDB). Similar results were detected in primary brain tumor patients using N3C. The odds of undergoing surgical procedures in patients resided in the higher density of COVID-19 prevalence (four zip code-level, per 1000 population) (aOR-0.63, 0.69, 0.59, all p&amp;lt; 0.001) and with COVID-19 positivity (aOR-0.54, p&amp;lt; 0.001) were significantly lower comparing to the related reference groups (N3C). CONCLUSIONS Our findings suggest that healthcare delivery for GBM and primary brain tumors has been remarkably affected by COVID-19 positivity and high-level COVID-19 prevalence during the pandemic.
DDDR-26. INHIBITION OF RAD52 ACTIVITY ENHANCES THE RADIOSENSITIVITY IN DIPG
Authors: Eita Uchida, Yukitomo Ishi, Jun Watanabe, Lu Wang, Hiam Abdala-Valencia, Samantha Gadd, Rintaro Hashizume
Journal: Neuro-Oncology (2023)

Abstract Diffuse intrinsic pontine glioma (DIPG) is one of the most devastating childhood cancers that limited response to radiation therapy, resulting in median overall survival of approximately 10 months. There is a critical need for new therapeutics that enhance the radiation effect while enabling the use of lower doses of radiation to limit long-term side effects in young patients. We, therefore, tested the hypothesis that targeting RAD52 activity sensitizes the radiation response of DIPG. Genome-wide CRISPR/Cas9 screening identified RAD52 as potential therapeutic target in DIPG cells. RAD52 inhibition, using shRNA mediated RAD52 depletion and treatment with RAD52 inhibitor, D-I03, suppressed DIPG cell proliferation. Importantly, RAD52 inhibition in combination with radiation therapy further increased radiosensitivity of DIPG cells. Immunocytochemistry of DNA double-strand breaks (DSB) marker γH2AX and repair marker 53BP1 showed that RAD52 inhibition sustained DNA damage with high levels of γH2AX at 24 hours following radiation while the level of 53BPI was decreased, thereby inhibiting DNA DSB repair. Western blotting also revealed that RAD52 inhibition causes a sustained level of phosphorylated Rad50 and γH2AX in irradiated DIPG cells. DNA repair assay showed that RAD52 inhibition suppressed DNA DSB repair through a homologous recombination pathway. RNA sequencing showed that RAD52 inhibition downregulated genes associated with the DNA repair pathway. Finally, the combination therapy of D-I03 RAD52 inhibitor and radiation inhibited tumor growth and significantly increased survival of mice bearing DIPG patient-derived xenografts, outperforming either monotherapy. Together, these results highlight RAD52 inhibitor as a potential radiosensitizer and provide a rationale for developing combination therapy with radiation in the treatment of DIPG.
EXTH-64. ESTABLISHING A CLINICALLY RELEVANT MOUSE MODEL OF MESENCHYMAL GLIOBLASTOMA FOR STUDYING TME TARGETING TREATMENTS
Authors: Kate Connor, Kieron White, James Clerkin, Liam Shiels, Kieron Sweeney, Thomas Van Brussel, Ingrid Arijs, Diether Lambrechts, Gautam Shankar, Frederik de Smet, Dieter Zopf, Stephen Maher, Laure Marignol, Patrick Dicker, Jochen Prehn, David O'Brien, Annette Byrne
Journal: Neuro-Oncology (2023)

Abstract Historically, pre-clinical GBM models have largely failed to predict response in the clinical setting. Here, we establish a more clinically faithful model using the syngeneic NFpp10a-Luc2 mesenchymal-GBM cell line to study response to resection and temozolomide (TMZ), adjuvant/neo-adjuvant anti-PD1 and Regorafenib (REGO) therapy. Cells were orthotopically implanted in C57BL/6-mice. Response to surgical and therapeutic interventions was assessed using bioluminescence imaging (BLI). Murine Microenvironment cell-population (mMCP)-counter, GSEA and multiple iteractive labelling by antibody neodeposition (MILAN, high-dimensional single-cell multiplex analysis) were employed to characterise treatment-related TME effects. We observed survival advantage in aged mice undergoing resection (resection:33.5 days vs non-resection:18 days; p = 0.0166). TMZ/anti-PD1 had no impact on tumour growth (TMZ: p = 0.9001, anti-PD1: p = 0.7933) or survival (TMZ:p = 0.3035, anti-PD1-:p = 0.6328). Neo-adjuvant anti-PD1 also conferred no survival advantage in young mice (33 vs 35 days; p = 0.9429). REGO/REGO+TMZ treatment conferred no survival benefit in young mice (REGO:p = 0.0735 and REGO+TMZ:p = 0.3945). mMCP-counter (which estimates the abundance of TME-cell populations from gene-expression data) showed resection upregulated B-cells and mast-cells, whereas TMZ caused a decreased abundance of vessels. Anti-PD1 treatment caused an enrichment of B-cells, mast-cells, and CXCR3 expression (p = 0.0045). REGO/TMZ+REGO treatment upregulated cytotoxic-lymphocyte populations. MILAN analysis showed resection increased cytotoxic-T-cells (20.3% vs pre-resection:7%). In contrast, TMZ/REGO monotherapy increased tumour-cells and decreased cytotoxic-T-cells. Anti-PD1 decreased macrophage abundance (39.8% vs control:14.5%). Likewise, TMZ+REGO decreased macrophages (11.3% vs control:35.3%) but upregulated B-cells and vessels. Overall, we have characterised response of the NFpp10a mouse model to resection, TMZ, anti-PD1 and REGO. We have shown that the model is insensitive to chemotherapy and TME-targeting therapies, mirroring patient-response patterns. Nevertheless, we observe transcriptomic and proteomic changes following TME-targeting treatments. Further analyses of these TME-associated resistance properties may help guide novel combinatorial treatment regimens. Overall, the NFpp10a model of mesenchymal GBM may be employed in future pre-clinical studies to accurately guide future clinical trials.
QLTI-01. HIGH-GRADE ASTROCYTOMA WITH PILOID FEATURES RESPONSE TO TREATMENT WITH CARBOPLATIN AND VINCRISTINE
Authors: Brandon Cielo
Journal: Neuro-Oncology (2023)

Abstract High-grade astrocytoma with piloid features (HGAP) is a brain tumor that requires distinct DNA methylation profiling for diagnosis. The current literature on HGAP response to treatment is limited. This case details the response to treatment of a young female patient initially with a pilocytic astrocytoma that at progression transformed into HGAP, both diagnoses confirmed with methylation testing. At 12 years old, the patient initially presented with unremitting headaches and syncopal episodes. Imaging revealed a non-enhancing non-cystic lesion in the roof of the fourth ventricle measuring 5 mm in the greatest dimension. She was followed by serial surveillance until undergoing surgical resection four years later. Histologically the tumor was grade I pilocytic astrocytoma containing a KIAA1549-BRAF fusion; the diagnosis was subsequently confirmed with methylation array testing. The patient transitioned to serial surveillance until she was lost to follow-up. At 27 years old, she presented with progressive headaches, gait instability, and agraphia. MRI revealed a posterior fossa cerebellar mass and surgical resection was performed. Histologically this was an anaplastic pilocytic astrocytoma with KIAA1549-BRAF fusion; however, DNA methylation profiling confirmed the diagnosis of HGAP. The patient was treated with postoperative radiation and demonstrated asymptomatic tumor progression in the left cerebellar hemisphere fourteen months later. She received carboplatin and vincristine with radiographic response and stability for four months until discontinuation due to tumor progression with infiltrative disease within the posterior fossa and brainstem. Her treatment was transitioned to selumetinib with mixed radiographic response but continued clinical deterioration after three months. Selumetinib was terminated and best supportive care was initiated. The patient died 216 months from initial presentation with pilocytic astrocytoma and 28 months from transformation into HGAP. To our knowledge, this is the first report of HGAP with treatment response to carboplatin and vincristine. Further research into the best treatments for HGAP is needed.
EXTH-81. RE-EXPRESSION OF CXCL9 FOLLOWING ADENO-ASSOCIATED VIRUS (AAV) TRANSGENE DELIVERY TRANSFORMS THE IMMUNOLOGICAL LANDSCAPE OF GLIOBLASTOMA, SENSITIZING TUMORS TO PD-1 IMMUNE CHECKPOINT BLOCKADE (ICB)
Authors: Christina von Roemeling, Oleg Yegorov, Changlin Yang, Rylynn Russell, Savannah Carpenter, Vrunda Trivedi, Alisha Bhatia, Bently Doonan, Todd Golde, Duane Mitchell
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND To date, few glioblastoma (GBM) patients have demonstrated clinical benefit from treatment with anti-PD-1 ICB. GBM is notoriously devoid of lymphocytes, signifying that a possible obstacle for effective ICB response may be the limited ability of cytotoxic T-lymphocytes (CTLs) to home to these tumors. CTLs are recruited via long-range signaling mediated by the diffusion of chemokines present in inflammatory environments. Following a comprehensive chemokine screen of clinical tumor specimens, we identified that CXC motif ligand 9 (CXCL9) is notably absent in GBM. To test if GBM reconstitution with CXCL9 could transform these intractable tumors into ICB-responsive, we leveraged AAV gene therapy to generate durable production of this potent lymphotactic signal. HYPOTHESIS AAV mediated re-expression of CXCL9 will improve lymphotaxis in GBM, sensitizing these tumors to PD-1 ICB. METHODS 3-dimensional whole brain fluorescent imaging was performed to characterize the distribution, tropism, and durability of AAV transgene expression in preclinical GBM models. Single-cell RNA sequencing (scRNAseq) and multiparameter flow cytometry was utilized to immunologically profile tumors in response to single and combination treatment. Survival studies with and without lymphocyte depletion were performed to evaluate immunogenic responsiveness of therapy. RESULTS Intra-tumor delivery of AAV6 yields stable transduction of tumor-reactive astrocytes, producing a localized, peri-tumoral pattern of transgene signal distribution. Combination therapy increases tumor infiltration by lymphocytes. scRNAseq analyses reveal widespread innate and adaptive immune activation in response to each CXCL9 and PD-1 ICB treatment. Infiltrating CD8 T-lymphocytes demonstrate inflammatory signatures associated with increased effector function, including antigen presentation, cytotoxicity, and TCR signaling. Combination treatment considerably improved overall survival in two distinct GBM models, with durable responses dependent on CD8 T-lymphocyte infiltration. CONCLUSIONS This work suggests direct conditioning of the tumor microenvironment by AAV-CXCL9 could potentially overcome a key resistance factor in GBM, sensitizing tumors to immune mediated therapies such as PD-1 ICB.
EXTH-61. A MULTI-TARGETED APPROACH TO EVALUATE THERAPEUTIC SELECTION AND EFFICACY IN PRECLINICAL GBM MODELS
Authors: Emily Eastwood, Bianca Carapia, Javier Rodriguez, Kristen Buck, Bridget Corcoran, Yuan-Hung Chien, Warren Andrews, Long Do, Jonathan Nakashima, Jantzen Sperry
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM) is a devastating primary brain cancer with approximately 10,000 new US diagnoses annually. The current standard of care for GBM includes surgical resection followed by radiation therapy (RT) and temozolomide (TMZ), however there is near universal recurrence and development of resistance after treatment. Relapse in disease is tightly linked with dynamic changes in gene expression during tumor evolution, highlighting the need for stronger preclinical GBM models. Here we report developing a pair of patient-derived xenograft (PDX) models from surgical resections obtained from initial GBM incidence in a patient (CRT00433) and subsequent recurrence following treatment (CRT00435) in order to study disease progression and novel treatment strategies. Recent studies have suggested the utilization of combination therapy approaches for GBM patients to address TMZ resistance. To this end, Certis has developed a personalized, AI-based approach to predict and test combination therapies for CRT00433/435. Accuracy of the predicted sensitivities to treatment was then evaluated in vivo using both subcutaneously and orthotopically engrafted mouse modeling. Luciferase-tagged CRT00433 and CRT00435 spheroid cell lines were transduced with firefly luciferase and implanted intracranially by stereotactic surgery for orthotopic monitoring. Optical bioluminescence imaging (BLI) and MRI were used to assess therapeutic response of AI-predicted combination therapies and standard of care (RT and/or TMZ). Both in-life imaging and terminal histologic analysis of the tumors confirmed high fidelity to several of the therapies tested. In all, these results demonstrate a novel, combinatorial platform with which to assess therapeutic efficacy in GBM and exploit the overall ability of this deadly disease to adapt to an ever-changing molecular and genetic landscape.
NIMG-32. MULTI-MODAL ANALYSIS UNCOVERS DIFFERENTIALLY REGULATED PATHWAYS ASSOCIATED WITH RADIO-PHENOTYPES IN PEDIATRIC LOW-GRADE GLIOMA
Authors: Anahita Fathi Kazerooni, Adam Kraya, Komal Rathi, Debanjan Haldar, Aria Mahtabfar, Nastaran Khalili, Ariana Familiar, Meen Chul Kim, Sina Bagheri, Hannah Anderson, Jeffrey B Ware, Phillip Storm, Christos Davatzikos, Arastoo Vossough, Adam Resnick, Ali Nabavizadeh
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Pediatric low-grade glioma is comprised of a broad variety of histological subtypes with heterogeneous responses to standard-of-care treatments. Understanding the biological pathways underlying clinical radiographic appearances, or radio-phenotypes, may facilitate precision diagnostics prior to the initiation of any interventions, thereby, reducing the risk of co-morbidities while improving patient outcome. Here, we aim to comprehensively harness the high-throughput multi-modal data available through Children’s Brain Tumor Network (CBTN) to elucidate the pathways that form radio-phenotypic traits of pLGG. METHODS On a cohort of 165 patients with pLGG, 881 radiomic features were extracted from multiparametric MRI sequences. We applied principal component analysis (PCA) followed by K-Means clustering to the radiomic features along with clinical variables of age, gender, and tumor location to group the patients into distinct imaging subtypes. We used whole transcriptomic data from OpenTargets to compare differential expression and co-expression of network- and pathway-level properties via Gene Set Enrichment Analysis (GSEA), and Gene Sets Net Correlations Analysis (GSNCA) among the discovered imaging subtypes. RESULTS Three imaging subtypes of pLGG were identified, among which subtype1 tumors showed increased proliferative capacity and invasive potential. This was suggested by higher expression of cell cycle regulatory, extracellular matrix (ECM) remodeling, and cell migratory pathways in subtype1 than subtypes 2 and 3. Furthermore, subtype1 exhibited differential TNF/TNFR signaling compared to subtype2, potentially related to differential regulation of pro-tumorigenic immune pathways, and differential regulation of TGF-beta and Aurora Kinase A signaling compared to subtype3, associated with differences in proliferative pathways. Subtypes 1 and 2 exhibit higher pro-tumorigenic cytokine expression while subtype3 involves higher expression of neurotransmitter release and neuronal activity, which may be targetable. CONCLUSIONS Our multi-modal radiogenomic analysis unraveled molecular underpinnings that give rise to the formation of distinct imaging phenotypes, with the potential to inform personalized treatments for children with brain tumors.
CNSC-26. GLIOBLASTOMA-NEURONAL CIRCUIT INTEGRATION IS MODULATED BY INTERLEUKIN-6
Authors: Andy Daniel, Saritha Krishna, Shawn Hervey-Jumper
Journal: Neuro-Oncology (2023)

Abstract The pleiotropic cytokine interleukin-6 (IL-6) is known to be involved in both pro- and anti-inflammatory signaling cascades. In glioblastoma studies using animal and human models, IL-6 promotes immunosuppression and tumor progression and is negatively associated with survival. Intriguingly, IL-6 also contributes to increased synaptogenesis during development and following focal brain injury. Glioblastoma remodeling of neuronal circuits influences patient survival; therefore, it is possible that IL-6 has mechanistic significance. Here, we investigated IL-6 as a driver of activity-dependent glioblastoma proliferation using patient-derived xenograft (PDX) mouse and human glioblastoma models. We assessed neuronal activity by microelectrode arrays and in vitro calcium imaging using weighted mean firing rate (WMFR), network burst frequency (NBF), and synchrony index. Next, we used bulk and single-cell RNA sequencing on 13,731 cells from ten tumors including pair-matched samples to identify differentially expressed genes in intratumoral regions with elevated functional connectivity and found IL6 to be highly upregulated. Mouse embryonic cortical neurons and cerebral organoids co-cultured with primary patient-derived glioblastoma cells demonstrated concentration-dependent neuronal hyperexcitability (increased WMFR and NBF) in IL-6-overexpressing conditions compared to the neuron-only condition. Pharmacological inhibition using the humanized IL-6 receptor antibody tocilizumab reduced network synchrony across models. These findings suggest that IL-6-induced glioma-neuronal hyperexcitability may be inhibited by the FDA-approved tocilizumab, thereby providing preclinical support for its use to treat activity-dependent mechanisms of glioblastoma proliferation. Future studies are needed to uncover mechanisms and clinical efficacy.
SURG-03. SURVIVAL STRATIFICATION OF IDH-WILDTYPE GLIOBLASTOMA IN THE MOLECULAR ERA: A RECURSIVE PARTITIONING ANALYSIS INCORPORATING EXTENT OF RESECTION OF CONTRAST-ENHANCING AND NON-ENHANCING TUMORS
Authors: Yae Won Park, Kyu Sung Choi, Ji Eun Park, Sung Soo Ahn, Jong Hee Chang
Journal: Neuro-Oncology (2023)

Abstract METHODS This multicenter cohort study included a development cohort of 622 IDH-wildtype glioblastoma patients from a single institution (diagnosed between 2001 and 2021) and 445 patients as validation cohorts from two institutions. All patients completed radiotherapy plus concurrent temozolomide and had complete information on IDH mutation and MGMT promoter methylation status. EOR of CE and NE tumors were evaluated. A RPA analysis was performed on behalf of results of the Cox proportional hazards model. The RPA model was compared with a previous RTOG RPA model. RESULTS In the developmental cohort, older age (hazard ratio [HR] = 1.02, P &amp;lt; 0.001), MGMT methylation (HR = 0.51, P &amp;lt; 0.001), KPS (HR = 0.98, P &amp;lt; 0.001), and EOR of CE and NE tumors (GTR of CE tumor and non-GTR of NE tumor, HR = 1.82, P &amp;lt; 0.001; non-GTR of both CE and NE tumor, HR = 2.05, P &amp;lt; 0.001; reference group as GTR of both CE and NE tumor) were independent prognostic factors on multivariable analysis. The novel RPA consisting of age, MGMT methylation, KPS, and EOR of CE and NE tumors revealed greater separation of prognostic classes compared with the previous RTOG RPA model. The prognostic significance of the novel RPA model was subsequently confirmed in the validation cohorts. CONCLUSION The RPA model in IDH-wildtype glioblastoma patients incorporating EOR of CE and NE tumors is a valid model. This simple RPA model has the potential to contribute to improving the accurate assessment of prognostic groups in IDH-wildtype glioblastoma patients and to influence clinical decision-making.